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Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

API method:

GET /api/packages?search=hello&page=1&limit=20

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r-oligo 1.74.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-affxparser@1.82.0 r-affyio@1.80.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bit@4.6.0 r-dbi@1.2.3 r-ff@4.5.2 r-oligoclasses@1.72.0 r-preprocesscore@1.72.0 r-rsqlite@2.4.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/oligo/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Preprocessing tools for oligonucleotide arrays
Description:

This package provides a package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

r-modstrings 1.26.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-crayon@1.5.3 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0 r-stringi@1.8.7 r-stringr@1.6.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Modstrings
Licenses: Artistic License 2.0
Build system: r
Synopsis: Working with modified nucleotide sequences
Description:

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionality for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

r-genomicalignments 1.46.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-cigarillo@1.0.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomicAlignments
Licenses: Artistic License 2.0
Build system: r
Synopsis: Representation and manipulation of short genomic alignments
Description:

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

r-pscbs 0.68.0
Propagated dependencies: r-aroma-light@3.40.0 r-dnacopy@1.84.0 r-future@1.68.0 r-matrixstats@1.5.0 r-r-cache@0.17.0 r-r-methodss3@1.8.2 r-r-oo@1.27.1 r-r-utils@2.13.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HenrikBengtsson/PSCBS
Licenses: GPL 2+
Build system: r
Synopsis: Analysis of parent-specific DNA copy numbers
Description:

This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

r-deco 1.13.0
Propagated dependencies: r-ade4@1.7-23 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocparallel@1.44.0 r-biocstyle@2.38.0 r-cluster@2.1.8.1 r-foreign@0.8-90 r-gdata@3.0.1 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gridextra@2.3 r-limma@3.66.0 r-locfit@1.5-9.12 r-made4@1.84.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-scatterplot3d@0.3-44 r-sfsmisc@1.1-23 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/fjcamlab/deco
Licenses: GPL 3+
Build system: r
Synopsis: Decomposing heterogeneous cohorts using omic data profiling
Description:

This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.

r-rots 2.2.0
Propagated dependencies: r-biobase@2.70.0 r-biocparallel@1.44.0 r-lme4@1.1-37 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ROTS/
Licenses: GPL 2+
Build system: r
Synopsis: Reproducibility-Optimized Test Statistic
Description:

This package provides tools for calculating the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

r-org-dm-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/org.Dm.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Fly
Description:

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

r-flowcore 2.22.0
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cpp11@0.5.2 r-cytolib@2.22.0 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rprotobuflib@2.22.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowCore
Licenses: Artistic License 2.0
Build system: r
Synopsis: Basic structures for flow cytometry data
Description:

This package provides S4 data structures and basic functions to deal with flow cytometry data.

r-bionero 1.18.0
Propagated dependencies: r-biocparallel@1.44.0 r-complexheatmap@2.26.0 r-dynamictreecut@1.63-1 r-genie3@1.32.0 r-ggdendro@0.2.0 r-ggnetwork@0.5.14 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-igraph@2.2.1 r-intergraph@2.0-4 r-matrixstats@1.5.0 r-minet@3.68.0 r-netrep@1.2.9 r-patchwork@1.3.2 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rlang@1.1.6 r-summarizedexperiment@1.40.0 r-sva@3.58.0 r-wgcna@1.73
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/almeidasilvaf/BioNERO
Licenses: GPL 3
Build system: r
Synopsis: Biological network reconstruction omnibus
Description:

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.

r-gqtlstats 1.21.3
Propagated dependencies: r-annotationdbi@1.72.0 r-batchjobs@1.10 r-bbmisc@1.13 r-beeswarm@0.4.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-doparallel@1.0.17 r-dplyr@1.1.4 r-erma@1.24.1 r-ffbase@0.13.3 r-foreach@1.5.2 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 r-ggbeeswarm@0.7.2 r-ggplot2@4.0.1 r-gqtlbase@1.21.1 r-hardyweinberg@1.7.9 r-homo-sapiens@1.3.1 r-iranges@2.44.0 r-limma@3.66.0 r-mgcv@1.9-4 r-plotly@4.11.0 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-shiny@1.11.1 r-snpstats@1.60.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gQTLstats
Licenses: Artistic License 2.0
Build system: r
Synopsis: Computationally efficient analysis for eQTL and allied studies
Description:

This package provides tools for the computationally efficient analysis of quantitative trait loci (QTL) data, including eQTL, mQTL, dsQTL, etc. The software in this package aims to support refinements and functional interpretation of members of a collection of association statistics on a family of feature/genome hypotheses.

r-singler 2.12.0
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/SingleR
Licenses: GPL 3
Build system: r
Synopsis: Reference-based single-cell RNA-seq annotation
Description:

This package performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

r-bicare 1.68.0
Propagated dependencies: r-biobase@2.70.0 r-go-db@3.22.0 r-gseabase@1.72.0 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr
Licenses: GPL 2
Build system: r
Synopsis: Biclustering analysis and results exploration
Description:

This is a package for biclustering analysis and exploration of results.

r-rtracklayer 1.70.0
Dependencies: curl@8.6.0 zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.56.0 r-biocio@1.20.0 r-biostrings@2.78.0 r-curl@7.0.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-httr@1.4.7 r-iranges@2.44.0 r-restfulr@0.0.16 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-xml@3.99-0.20 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rtracklayer
Licenses: Artistic License 2.0
Build system: r
Synopsis: R interface to genome browsers and their annotation tracks
Description:

rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

r-bayseq 2.44.0
Propagated dependencies: r-abind@1.4-8 r-edger@4.8.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/baySeq/
Licenses: GPL 3
Build system: r
Synopsis: Bayesian analysis of differential expression patterns in count data
Description:

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

r-jetset 3.4.0
Propagated dependencies: r-annotationdbi@1.72.0 r-org-hs-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.cbs.dtu.dk/biotools/jetset/
Licenses: Artistic License 2.0
Build system: r
Synopsis: One-to-one gene-probeset mapping for Affymetrix human microarrays
Description:

This package provides a one-to-one mapping from gene to "best" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene "signature" that is defined by gene names rather than by specific probe sets. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.

r-acme 2.66.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/aCGH/
Licenses: GPL 2+
Build system: r
Synopsis: Calculating microarray enrichment
Description:

This package implements algorithms for calculating microarray enrichment (ACME), and it is a set of tools for analysing tiling array of combined chromatin immunoprecipitation with DNA microarray (ChIP/chip), DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

r-anaquin 2.34.0
Propagated dependencies: r-deseq2@1.50.2 r-ggplot2@4.0.1 r-knitr@1.50 r-locfit@1.5-9.12 r-plyr@1.8.9 r-qvalue@2.42.0 r-rocr@1.0-11
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.sequinstandards.com/
Licenses: Modified BSD
Build system: r
Synopsis: Statistical analysis of sequins
Description:

The project is intended to support the use of sequins(synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard library for quantitative analysis, modelling, and visualization of spike-in controls.

r-basicstarrseq 1.38.0
Propagated dependencies: r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BasicSTARRseq
Licenses: LGPL 3
Build system: r
Synopsis: Basic peak calling on STARR-seq data
Description:

This package implements a method that aims to identify enhancers on large scale. The STARR-seq data consists of two sequencing datasets of the same targets in a specific genome. The input sequences show which regions where tested for enhancers. Significant enriched peaks i.e. a lot more sequences in one region than in the input where enhancers in the genomic DNA are, can be identified. So the approach pursued is to call peak every region in which there is a lot more (significant in a binomial model) STARR-seq signal than input signal and propose an enhancer at that very same position. Enhancers then are called weak or strong dependent of there degree of enrichment in comparison to input.

r-samr 3.0
Propagated dependencies: r-gsa@1.03.3 r-impute@1.84.0 r-matrixstats@1.5.0 r-openxlsx@4.2.8.1 r-shiny@1.11.1 r-shinyfiles@0.9.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://statweb.stanford.edu/~tibs/SAM/
Licenses: LGPL 3+
Build system: r
Synopsis: Significance analysis of Microarrays
Description:

This is a package for significance analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

r-methylkit 1.36.0
Propagated dependencies: r-data-table@1.17.8 r-emdbook@1.3.14 r-fastseg@1.56.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-kernsmooth@2.23-26 r-limma@3.66.0 r-mclust@6.1.2 r-mgcv@1.9-4 r-qvalue@2.42.0 r-r-utils@2.13.0 r-rcpp@1.1.0 r-rhtslib@3.6.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/al2na/methylKit
Licenses: Artistic License 2.0
Build system: r
Synopsis: DNA methylation analysis from high-throughput bisulfite sequencing results
Description:

MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from Reduced representation bisulfite sequencing (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.

r-do-db 2.9
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DO.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation maps describing the entire Disease Ontology
Description:

This package provides a set of annotation maps describing the entire Disease Ontology.

r-cytoml 2.22.0
Dependencies: libxml2@2.14.6 zlib@1.3.1
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-cpp11@0.5.2 r-cytolib@2.22.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-flowcore@2.22.0 r-flowworkspace@4.22.0 r-ggcyto@1.38.0 r-graph@1.88.0 r-jsonlite@2.0.0 r-opencyto@2.22.0 r-rbgl@1.86.0 r-rgraphviz@2.54.0 r-rhdf5lib@1.32.0 r-rprotobuflib@2.22.0 r-tibble@3.3.0 r-xml@3.99-0.20 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RGLab/CytoML
Licenses: Artistic License 2.0
Build system: r
Synopsis: GatingML interface for cross platform cytometry data sharing
Description:

This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

r-somaticsignatures 2.46.0
Propagated dependencies: r-biobase@2.70.0 r-biostrings@2.78.0 r-genomicranges@1.62.0 r-ggbio@1.58.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-nmf@0.28 r-pcamethods@2.2.0 r-proxy@0.4-27 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/juliangehring/SomaticSignatures
Licenses: Expat
Build system: r
Synopsis: Somatic signatures
Description:

This package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

r-bisquerna 1.0.5
Propagated dependencies: r-biobase@2.70.0 r-limsolve@2.0.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.biorxiv.org/content/10.1101/669911v1
Licenses: GPL 3
Build system: r
Synopsis: Decomposition of bulk expression with single-cell sequencing
Description:

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.

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